From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Tue, 17 Sep 2013 16:12:56 +0000 (+0100)
Subject: Add reference on Jronn
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=847ba4b538be695e1408fd9251d60792415e30cf;p=jabaws.git

Add reference on Jronn
---

diff --git a/website/index.html b/website/index.html
index 4dd5d80..b2812e7 100644
--- a/website/index.html
+++ b/website/index.html
@@ -43,17 +43,18 @@
 <div id="content">
 <h2 id="headtitle">JABAWS 2.1</h2>
 <p style="color:black; font-weight:normal; text-align:left;"><span style="border-bottom:dotted 1px #666" title="JAva Bioinformatics Analysis Web Services">JABAWS</span> 
-is free software which provides <a href="http://en.wikipedia.org/wiki/Web_service">web services</a> conveniently packaged to run on your local computer, server, cluster or Amazon EC2 instance. Services for multiple sequence alignment 
-include <a href="http://www.clustal.org/omega">Clustal Omega</a>, <a href="http://www.clustal.org/clustal2">Clustal W</a>, 
+is free software which provides <a href="http://en.wikipedia.org/wiki/Web_service">web services</a> conveniently packaged to run on your local computer, server, cluster or Amazon EC2 instance. 
+Services for multiple sequence alignment include <a href="http://www.clustal.org/omega">Clustal Omega</a>, <a href="http://www.clustal.org/clustal2">Clustal W</a>, 
 <a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a>, <a href="http://www.drive5.com/muscle">MUSCLE</a>, 
 <a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">TCOFFEE</a> and <a href="http://probcons.stanford.edu/">PROBCONS</a>. Analysis services allow
-prediction of the protein secondary structure with <a href="http://www.compbio.dundee.ac.uk/www-jpred/">Jpred</a> and protein disorder with <a href="http://dis.embl.de/">DisEMBL</a>, <a href="http://iupred.enzim.hu">IUPred</a>, 
-<a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a> and <a href="http://globplot.embl.de/">GlobPlot</a>; 
-and calculation of amino acid alignment conservation with <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>. The secondary structure for an RNA aligment is possible with 
-the RNAalifold program from the <a href="http://www.tbi.univie.ac.at/RNA">Vienna RNA package</a>.
+prediction of the protein secondary structure with <a href="http://www.compbio.dundee.ac.uk/www-jpred/">Jpred</a> and protein disorder with <a href="http://dis.embl.de/">DisEMBL</a>, 
+<a href="http://iupred.enzim.hu">IUPred</a>,  Jronn (a Java implementation of <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a> by P. Troshin and G. Barton, unpublished), 
+and <a href="http://globplot.embl.de/">GlobPlot</a>; and calculation of amino acid alignment conservation with <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>. The 
+secondary structure for an RNA aligment can be predicted with the RNAalifold program from the <a href="http://www.tbi.univie.ac.at/RNA">Vienna RNA package</a>.
 </p><p> 
 <span style="color:black; font-weight:normal; text-align:left;">
-JABA 2.1 Web Services installations can be accessed from the <strong><a href="http://www.jalview.org">Jalview</a> desktop application</strong> (version 2.8 onwards) and the <strong>JABAWS command-line client</strong>, and provide multiple alignment 
+JABA 2.1 Web Services installations can be accessed from the <strong><a href="http://www.jalview.org">Jalview</a> desktop application</strong> (version 2.8 onwards) 
+and the <strong>JABAWS command-line client</strong>, and provide multiple alignment 
 and sequence analysis calculations limited only by your own computing resources.<br />
 </span></p>
 <div id="mainpagefeatures">
diff --git a/website/man_about.html b/website/man_about.html
index 46a7134..2c72efc 100644
--- a/website/man_about.html
+++ b/website/man_about.html
@@ -112,7 +112,7 @@
   <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>
   <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>
 </ul>
-<p>Protein Secondary structure</p>
+<p>Protein Secondary structure prediction</p>
 <ul>
   <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.compbio.dundee.ac.uk/www-jpred">Jpred</a></span> (3.0.3) </li>
 </ul>
@@ -121,7 +121,7 @@
 <ul>
   <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://dis.embl.de/">DisEMBL</a></span> (1.5) </li>
   <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://iupred.enzim.hu">IUPred</a></span> (1.0) </li>
-  <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a></span> (3.1) </li>
+  <li><span style="color:black; font-weight:normal; text-align:left;">Jronn - Java implementation of <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a></span> (3.1) </li>
   <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://globplot.embl.de/">GlobPlot</a></span> (2.3) </li>
   </ul>
 <p>Amino Acid conservation</p>
@@ -133,7 +133,7 @@
   <li><span style="color:black; font-weight:normal; text-align:left;">RNAalifold from <a href="http://www.tbi.univie.ac.at/RNA">ViennaRNA</a></span> (2.0) </li>
 </ul>
 
-
+All these codes including Jronn and AAcon are available at the <a href="http://www.compbio.dundee.ac.uk/download">Download</a> section (registration is required).
 
 <h3><a name="jaba2.1"/></a>What is new in JABAWS 2.1? </h3>
 <strong>JABAWS Version 2.1 (Released 1st Oct 2013)</strong><p>JABAWS 2.1 includes several bug fixes and minor updates for <a href="#jaba2">JABAWS Version 2.0</a>. These are listed below:</p>